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A DNase footprinting assay [1] is a DNA footprinting technique used in molecular biology/biochemistry that detects DNA-protein interaction by leveraging the fact that a protein bound to DNA often protects it from enzymatic cleavage. This makes it possible to locate a protein binding site on a particular DNA molecule.
DNase I cleaves DNA to form two oligonucleotide-end products with 5’-phospho and 3’-hydroxy ends and is produced mainly by organs of the digestive system. The DNase I family requires Ca2+ and Mg2+ cations as activators and selectively expressed. [1] In terms of pH, the DNAses I family is active in normal pH of around 6.5 to 8.
In vivo footprinting is a technique used to analyze the protein-DNA interactions that are occurring in a cell at a given time point. [16] [20] DNase I can be used as a cleavage agent if the cellular membrane has been permeabilized. However the most common cleavage agent used is UV irradiation because it penetrates the cell membrane without ...
In genetics, DNase I hypersensitive sites (DHSs) are regions of chromatin that are sensitive to cleavage by the DNase I enzyme. In these specific regions of the genome, chromatin has lost its condensed structure, exposing the DNA and making it accessible. This raises the availability of DNA to degradation by enzymes, such as DNase I.
In genetics, a hypersensitive site is a short region of chromatin and is detected by its super sensitivity to cleavage by DNase I and other various nucleases (DNase II and micrococcal nucleases). In a hypersensitive site, the nucleosomal structure is less compacted, increasing the availability of the DNA to binding by proteins, such as ...
DNase agar is used to test whether a microbe can produce the exoenzyme deoxyribonuclease (DNase), which hydrolyzes DNA. Methyl green is used as an indicator in the growth medium because it is a cation that provides an opaqueness to a medium with the presence of negatively charged DNA strands. When DNA is cleaved, the media becomes clear ...
The commonly used notation for restriction endonucleases [6] is of the form "VwxyZ", where "Vwx" are, in italics, the first letter of the genus and the first two letters of the species where this restriction endonuclease may be found, for example, Escherichia coli, Eco, and Haemophilus influenzae, Hin.
At sufficient concentrations, DNase I is capable of digesting nucleosome-bound DNA to 10bp, whereas micrococcal nuclease cannot. [17] Additionally, DNase-seq is used to identify DHSs, which are regions of DNA that are hypersensitive to DNase treatment and are often indicative of regulatory regions (e.g. promoters or enhancers). [57]